Creating a conda env within windows subsystem for linux

17 hours ago 1
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I have just started using windows subsystem for linux. I have a yml file that i am using to make the env proteomics_skani, called from within WSL, with the yml file living in my windows filesystem:

name: proteomics_skani dependencies: - python=3.10 - pandas - numpy - requests - pip - scipy - spyder - bioconda::skani - conda-forge::networkx=3.1 - pip=22.3.1 - pip: - plotly==5.24.1 - pytest==8.2.2

I need to use Skani in my code, which only runs on linux. I am running this command to make my env within WSL, so I can open Spyder from within WSL in that env, and call the Skani program with subprocess from within python. However, I get an error:

(base) username@my-id:/mnt/c/Users/username$ conda create --file "mnt/c/Users/username/OneDrive - myUniversity/Desktop/proteomics_skani.yml" 2 channel Terms of Service accepted Retrieving notices: done ArgumentError: one of the arguments -n/--name -p/--prefix is required

Can someone point me to the issue? I guess it would be better to store the yml file in the WSL directory/OS, but have no idea where it should go (just the base folder for \\wsl.localhost\Ubuntu-24.04?).

Thanks!

Tim

EDIT

I got told the updated conda version was already installed, which is interesting, as it also says I have the problematic version and a newer one is available:

(base) username@my-id:/mnt/c/Users/username$ conda -V conda 26.1.1 (base) username@my-id:/mnt/c/Users/username$ conda update --name base conda 2 channel Terms of Service accepted Channels: - defaults Platform: linux-64 Collecting package metadata (repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 26.1.1 latest version: 26.3.2 Please update conda by running $ conda update -n base -c defaults conda # All requested packages already installed. (base) username@my-id:/mnt/c/Users/username$ conda update -n base -c defaults conda 2 channel Terms of Service accepted Channels: - defaults Platform: linux-64 Collecting package metadata (repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 26.1.1 latest version: 26.3.2 Please update conda by running $ conda update -n base -c defaults conda # All requested packages already installed. (base) username@my-id:/mnt/c/Users/username$ conda -V conda 26.1.1
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